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[gofriends] GO tool recommendations needed for demo to ~80 biologists new to GO.

Sorin Draghici sod at cs.wayne.edu
Fri Oct 5 12:59:16 PDT 2007


Emily,


Before going ahead and spend hours trying each of the over 20 tools
available in this area, you may want to read a paper reviewing such tools:

http://vortex.cs.wayne.edu/papers/Ontological_analysis.pdf

Two more points:
1) The statistical significance you desire can only be calculated with
respect to some reference set of genes. This is because the p-value
represents the probability of obtaining those GO categories if you were
to pick random genes from this reference list. So, besides your input,
you need to provide such a reference file. For instance, if you used a
specific microarray or protein array to monitor the expression levels of
these proteins, the list of genes on that array would be the reference
list that you need.

2) Secondly, you should be aware that the results of this type of
analysis _can_ be influenced (although they shouldn't) by both the type
of IDs you use as input, as well as by the source of the annotations.
Here is a link to a paper discussing these issues:

http://vortex.cs.wayne.edu/papers/Babel.tower.pdf

and here is a pointer to a tool, Onto-Translate, that can help you
translate between different types of IDs:

http://vortex.cs.wayne.edu/ontoexpress/

This work has been supported by several NSF and NIH grants so a (free)
registration is required for grant accounting purposes only.

Best regards,



Sorin Draghici, Ph.D.


Director of the Bioinformatics Core, Karmanos Cancer Institute

Associate Professor		Tel: (313) 577-5484
Dept. of Computer Science	Fax: (313) 577-6868
Wayne State University
5143 Cass Ave, Room 431 State Hall,
Detroit, MI, 48202
WWW: http://vortex.cs.wayne.edu/Sorin/ (personal)
WWW: http://vortex.cs.wayne.edu/Projects.html (lab)


Check out my recent book: Data Analysis Tools for Microarrays:
http://www.crcpress.com/shopping_cart/products/product_detail.asp?sku=C3154&parent_id=&pc=



E Dimmer wrote:
> Hi,
> 
> I'm looking for a tool to demonstrate during a couple of  'Introduction
> to GO' talks/tutorials and I would be extremely grateful if some tool
> developers/users could help me choose one.
> 
> As the audience would be mainly composed of biologists looking at
> resources that work with UniProt data, I'm looking for an online tool
> that clusters UniProt protein accessions to display  over-representation
> of GO terms. I need a simple, effective tool that:
> 
> 1. is freely available
> 
> 2. can accept human UniProt Accession numbers as input (e.g. Q9Y5Q8)
> 
> 3. can temporarily cope with the load of ~ 40 people accessing the tool
> simultaneously (if the tool can alternatively be locally installed,
> thats fine too)
> 
> 4. provides a simple interface and outputs a graphic showing showing
> clustering of proteins around a GO node (if the tool can do more that's
> fine, but for the limited time-span of the tutorials I need users to
> easily understand the main idea of the tool and have results returned
> quickly)
> 
> 5. finds statistical significance using a multiple-testing correction
> 
> 6. appreciates the GO DAG, GO evidence codes, and has removed 'NOT'
> annotations from any imported GO annotations.
> 
> 7.  provides full documentation and is fully supported
> 
> 8. updates regularly with the GO gene association and OBO files (monthly
> would be ideal)
> 
> If you have/use a tool which meets all these requirements, could you
> please let me know?
> 
> At the bottom of this e-mail I have listed 55 human UniProt Accessions
> which all have an annotation to the GO term 'Notch signaling pathway'
> (GO:0007219) or one of its children, an example of one of the dataset I
> might supply for the demo.
> 
> If I find more than one tool that meets the above requirements, I will
> at least advertise them all, even if I can not demo each of them.
> 
> Thanks very much,
> 
> Emily
> 
> **
> 
> O00548
> O14672
> P05067
> P25963
> P46531
> P49768
> P49810
> P50553
> P78504
> P78536
> Q04721
> Q06330
> Q0VG99
> Q12860
> Q12948
> Q16873
> Q4KMR2
> Q59ED8
> Q5SPL1
> Q5SSY7
> Q5STG5
> Q5SXM3
> Q5VTD0
> Q86UW9
> Q86Y01
> Q86YT6
> Q8IZL2
> Q8N9I9
> Q8NBS4
> Q8NFT8
> Q8WW43
> Q92542
> Q92585
> Q96AX9
> Q96BI3
> Q96JK9
> Q96T58
> Q99466
> Q99958
> Q9BRJ9
> Q9BYE0
> Q9H3D4
> Q9H488
> Q9HD90
> Q9NQ87
> Q9NR61
> Q9NYJ7
> Q9NZ42
> Q9UBP5
> Q9UBV2
> Q9UM47
> Q9UQ52
> Q9Y219
> Q9Y2E6
> Q9Y5J3
> 

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